├── LICENSE # MIT license
├── README.md # Quick-start overview
├── structure.md # Original structural map
├── STRUCTURE_v2.md # Enhanced structural map with field theory
├── context.json # Original schema configuration
├── context_v2.json # Extended schema with field protocols
├── context_v3.json # Neural field extensions
├── context_v3.5.json # Symbolic mechanism integration
├── CITATIONS.md # Research references and bridges
├── 00_foundations/ # First-principles theory
│ ├── 01_atoms_prompting.md # Atomic instruction units
│ ├── 02_molecules_context.md # Few-shot examples/context
│ ├── 03_cells_memory.md # Stateful conversation layers
│ ├── 04_organs_applications.md # Multi-step control flows
│ ├── 05_cognitive_tools.md # Mental model extensions
│ ├── 06_advanced_applications.md # Real-world implementations
│ ├── 07_prompt_programming.md # Code-like reasoning patterns
│ ├── 08_neural_fields_foundations.md # Context as continuous fields
│ ├── 09_persistence_and_resonance.md # Field dynamics and attractors
│ ├── 10_field_orchestration.md # Coordinating multiple fields
│ ├── 11_emergence_and_attractor_dynamics.md # Emergent properties
│ │── 12_symbolic_mechanisms.md # Symbolic reasoning in LLMs
│ ├── 13_quantum_semantics.md # Multiple meanings (Superposition)
│ └── 14_unified_field_theory.md # Integrating theory models
├── 10_guides_zero_to_hero/ # Hands-on tutorials
│ ├── 01_min_prompt.ipynb # Minimal prompt experiments
│ ├── 02_expand_context.ipynb # Context expansion techniques
│ ├── 03_control_loops.ipynb # Flow control mechanisms
│ ├── 04_rag_recipes.ipynb # Retrieval-augmented patterns
│ ├── 05_protocol_bootstrap.ipynb # Field protocol bootstrap
│ ├── 06_protocol_token_budget.ipynb # Protocol efficiency
│ ├── 07_streaming_context.ipynb # Real-time context
│ ├── 08_emergence_detection.ipynb # Detecting emergence
│ ├── 09_residue_tracking.ipynb # Tracking symbolic residue
│ └── 10_attractor_formation.ipynb # Creating field attractors
├── 20_templates/ # Reusable components
│ ├── minimal_context.yaml # Base context structure
│ ├── control_loop.py # Orchestration template
│ ├── scoring_functions.py # Evaluation metrics
│ ├── prompt_program_template.py # Program structure template
│ ├── schema_template.yaml # Schema definition template
│ ├── recursive_framework.py # Recursive context template
│ ├── field_protocol_shells.py # Field protocol templates
│ ├── symbolic_residue_tracker.py # Residue tracking tools
│ ├── context_audit.py # Context analysis tool
│ ├── shell_runner.py # Protocol shell runner
│ ├── resonance_measurement.py # Field resonance metrics
│ ├── attractor_detection.py # Attractor analysis tools
│ ├── boundary_dynamics.py # Boundary operation tools
│ └── emergence_metrics.py # Emergence measurement
├── 30_examples/ # Practical implementations
│ ├── 00_toy_chatbot/ # Simple conversation agent
│ ├── 01_data_annotator/ # Data labeling system
│ ├── 02_multi_agent_orchestrator/ # Agent collaboration system
│ ├── 03_vscode_helper/ # IDE integration
│ ├── 04_rag_minimal/ # Minimal RAG implementation
│ ├── 05_streaming_window/ # Real-time context demo
│ ├── 06_residue_scanner/ # Symbolic residue demo
│ ├── 07_attractor_visualizer/ # Field visualization
│ ├── 08_field_protocol_demo/ # Protocol demonstration
│ └── 09_emergence_lab/ # Emergence experimentation
├── 40_reference/ # Deep-dive documentation
│ ├── token_budgeting.md # Token optimization strategies
│ ├── retrieval_indexing.md # Retrieval system design
│ ├── eval_checklist.md # PR evaluation criteria
│ ├── cognitive_patterns.md # Reasoning pattern catalog
│ ├── schema_cookbook.md # Schema pattern collection
│ ├── patterns.md # Context pattern library
│ ├── field_mapping.md # Field theory fundamentals
│ ├── symbolic_residue_types.md # Residue classification
│ ├── attractor_dynamics.md # Attractor theory and practice
│ ├── emergence_signatures.md # Detecting emergence
│ └── boundary_operations.md # Boundary management guide
├── 50_contrib/ # Community contributions
│ └── README.md # Contribution guidelines
├── 60_protocols/ # Protocol shells and frameworks
│ ├── README.md # Protocol overview
│ ├── shells/ # Protocol shell definitions
│ │ ├── attractor.co.emerge.shell # Attractor co-emergence
│ │ ├── recursive.emergence.shell # Recursive field emergence
│ │ ├── recursive.memory.attractor.shell # Memory persistence
│ │ ├── field.resonance.scaffold.shell # Field resonance
│ │ ├── field.self_repair.shell # Self-repair mechanisms
│ │ └── context.memory.persistence.attractor.shell # Context persistence
│ ├── digests/ # Simplified protocol documentation
│ └── schemas/ # Protocol schemas
│ ├── fractalRepoContext.v3.5.json # Repository context
│ ├── fractalConsciousnessField.v1.json # Field schema
│ ├── protocolShell.v1.json # Shell schema
│ ├── symbolicResidue.v1.json # Residue schema
│ └── attractorDynamics.v1.json # Attractor schema
├── 70_agents/ # Agent demonstrations
│ ├── README.md # Agent overview
│ ├── 01_residue_scanner/ # Symbolic residue detection
│ ├── 02_self_repair_loop/ # Self-repair protocol
│ ├── 03_attractor_modulator/ # Attractor dynamics
│ ├── 04_boundary_adapter/ # Dynamic boundary tuning
│ └── 05_field_resonance_tuner/ # Field resonance optimization
├── 80_field_integration/ # Complete field projects
│ ├── README.md # Integration overview
│ ├── 00_protocol_ide_helper/ # Protocol development tools
│ ├── 01_context_engineering_assistant/ # Field-based assistant
│ ├── 02_recursive_reasoning_system/ # Recursive reasoning
│ ├── 03_emergent_field_laboratory/ # Field experimentation
│ └── 04_symbolic_reasoning_engine/ # Symbolic mechanisms
├── cognitive-tools/ # Advanced cognitive framework
│ ├── README.md # Overview and quick-start guide
│ ├── cognitive-templates/ # Templates for reasoning
│ │ ├── understanding.md # Comprehension operations
│ │ ├── reasoning.md # Analytical operations
│ │ ├── verification.md # Checking and validation
│ │ ├── composition.md # Combining multiple tools
│ │ └── emergence.md # Emergent reasoning patterns
│ ├── cognitive-programs/ # Structured prompt programs
│ │ ├── basic-programs.md # Fundamental program structures
│ │ ├── advanced-programs.md # Complex program architectures
│ │ ├── program-library.py # Python implementations
│ │ ├── program-examples.ipynb # Interactive examples
│ │ └── emergence-programs.md # Emergent program patterns
│ ├── cognitive-schemas/ # Knowledge representations
│ │ ├── user-schemas.md # User information schemas
│ │ ├── domain-schemas.md # Domain knowledge schemas
│ │ ├── task-schemas.md # Reasoning task schemas
│ │ ├── schema-library.yaml # Reusable schema library
│ │ └── field-schemas.md # Field representation schemas
│ ├── cognitive-architectures/ # Complete reasoning systems
│ │ ├── solver-architecture.md # Problem-solving systems
│ │ ├── tutor-architecture.md # Educational systems
│ │ ├── research-architecture.md # Information synthesis
│ │ ├── architecture-examples.py # Implementation examples
│ │ └── field-architecture.md # Field-based architectures
│ └── integration/ # Integration patterns
│ ├── with-rag.md # Integration with retrieval
│ ├── with-memory.md # Integration with memory
│ ├── with-agents.md # Integration with agents
│ ├── evaluation-metrics.md # Effectiveness measurement
│ └── with-fields.md # Integration with field protocols
└── .github/ # GitHub configuration
├── CONTRIBUTING.md # Contribution guidelines
├── workflows/ci.yml # CI pipeline configuration
├── workflows/eval.yml # Evaluation automation
└── workflows/protocol_tests.yml # Protocol testing